Release Notes can be found here.
FireCloud Error: processing-for-variant-discovery-gatk4
I tried to run the method "processing-for-variant-discovery-gatk4" cloned from the featured workspace "Germline-SNPs-Indels-GATK4-b37" on some of my samples. I only made 2 changes to the configuration: ref_name changed from "hg38" to "b37", and sample_name changed from "NA12878" to this.sample_id. I got the following error:
"Failed to evaluate 'PreProcessingForVariantDiscovery_GATK4.flowcell_unmapped_bams' (reason 1 of 1): Evaluating read_lines(flowcell_unmapped_bams_list) failed: java.io.IOException: Could not read from gs://fc-d2239f7f-d4b9-45de-a3bb-49a002f0bc1e/uBAM/N0.unmapped.bam: File gs://fc-d2239f7f-d4b9-45de-a3bb-49a002f0bc1e/uBAM/N0.unmapped.bam is larger than 10000000 Bytes. Maximum read limits can be adjusted in the configuration under system.input-read-limits."
I don’t see any variable named system.input-read-limits in the method configuration. Can you please help me out?
Also, my samples are from whole exome sequencing instead of whole genome sequencing, do I need to make any other changes to the configuration?